Build version: v1.3.1.1 Beta + Expansion and all DLCs
Severity: Medium
Annoyance factor: Through the roof!

Confusion for new players: High
Saved game: (2nd save in the 2nd post below)
In the save 2796-01-02, you can see that I had given a manual order to a Carrier (Overpowering Invader; part of 5th fleet) to refuel at Kygnos (after which, I re-automated it, so it would join the rest of the fleet AFTER having refueled).
N.B.: The fleet you see in the Kygnos system in the screenshot above is NOT 5th Fleet: it’s 2nd Fleet.
But in the 2796-04-22 save (in the post below), you can see that the carrier is now moving toward 5th fleet flagship, without having refueled at Kygnos 3 (where there’s plenty of fuel). And that, without me having given any order to 5th Fleet (which is in manual mode)!

So it looks as though the re-automation of the ship after the manual order resulted in it eventually canceling the manual order I had given to the ship!
That is one of the most annoying thing that can happen in the game: giving a manual order to a ship (or a fleet), and the game canceling that order, without reason nor notification!
Don’t know if it’s already the case or not, but if it isn’t, there should be 2 types of orders (or missions) internally in the game: manual and automated. And manual orders should never be canceled by the game, unless there’s a damn good reason to do so (and, ideally, there should be a notification about it in the rare cases when it would be justified).